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extend File-Formats.md with mutational signature datatype
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MatthijsPon committed May 17, 2023
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4 changes: 2 additions & 2 deletions docs/File-Formats.md
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Expand Up @@ -1609,7 +1609,7 @@ The mutational signature meta files follow the same convention as the [Generic A
however there are some key differences:
- `genetic_assay_type` should be set to `MUTATIONAL_SIGNATURE`
- `stable_id` values should end with: `{datatype}_{identifier}`, where:
- `datatype` is one of `contribution`, `pvalue` or `matrix`
- `datatype` is either `contribution`, `pvalue` or `matrix`
- `identifier` is consistent between files belonging to the same analysis
- Multiple signatures can be added to a single study, as long as they have different identifiers in their stable id (e.g., `contribution_SBS` and `contribution_DBS`)
- In `generic_entity_meta_properties` the `NAME` value is required. The `DESCRIPTION` and `URL` values can be added
Expand All @@ -1623,7 +1623,7 @@ Each collection of mutational signatures can consist of up to three different da
- Signature p-values file (optional)
- Data file containing p-values for each signature-sample pair. Values below 0.05 will be treated as significant.
- Mutation matrix file (optional)
- Data file containing nucleotide changes of a sample. cBioPortal has specific visualisation options for single-base substitutions (96 channels), double-base substitutions (72 channels) and insertion/deletions (83 channels), following the signatures defined by [COSMIC](https://cancer.sanger.ac.uk/signatures/). But other channels can also be used. Values are expected to be positive integers.
- Data file containing nucleotide changes of a sample. cBioPortal has specific visualization options for single-base substitutions (96 channels), double-base substitutions (72 channels) and insertion/deletions (83 channels), following the signatures defined by [COSMIC](https://cancer.sanger.ac.uk/signatures/). But other channels can also be used. Values are expected to be positive integers.

## Resource Data

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